Resident Eva
by ReiSnatcher
Summary: My name is Rei, and I remember everything. Next Chapter up. Shinji finds out what happened to Rei, and he'l do anything ot save her.
1. Prologue

**Prologue**

When Shinji Ikari woke up, the first thing he saw was the hospital ceiling overhead. The sight of it always made him depressed, since it always meant that he had just come from battling an angel in Unit One. Shinji thought and tried to remember why he was here this time, since his memory was a little fuzzy.

Suddenly several images flashed through his mind. The Fourteenth Angel entering the Geofront despite NERV's defenses; the head of Unit Two crashing into the shelter he had been hiding in; Unit Zero sacrificing with N2 mine to attempt and destroy the target; Unit Zero enveloped in a bright light as the mine went off; the angel slowly advancing past the still body of Unit Zero…

_That's right!_ Shinji thought. _Asuka! Ayanami! Are they alright! I must have defeated the angel if I'm here, but are they all right?_

"You are awake," a voice said, and Shinji turned to its blue-haired owner, who was sitting in a chair to his left.

"Ayanami!" he said. "You're all right!"

Rei looked at Shinji, happy for his concern, but she didn't let it show on her face. She never did, but she had been finding it harder and harder to contain her emotions around Shinji. She remembered that Shinji's friend, Suzuhara had told her that she had a thing for Shinji. Although Rei was ignorant to most thing, she knew from what she had over heard from other students that it meant she loved Shinji. She was sure, but she thought that Suzuhara was right. She hadn't been able to stop worrying about Shinji when he was absorbed into Unit One.

"Yes, I am fine." she said.

"What about Asuka?" he asked. "Is she alright too?"

"Pilot Soryu is well," Rei said, feeling a twinge of… something. She did not like it that Shinji was worried about the Second Child as well.

Shinji sighed in relief. "That's good," he said. "What happened? I can't seem to remember anything after I saw the N2 mine explode…" Suddenly, Shinji remembered something. He sat up, leaned over and grabbed Ayanami's shoulders. "Why did you do that!" he asked. "You could have died!"

Rei was momentarily shocked by Shinji's uncharacteristic outburst. She was confused when she saw the fear and anger in his face, and the tears beginning to form in his eyes. "It was the only possible way to defeat the angel," she said, and then she looked away from Shinji's gaze. It made her feel… odd. "And I can be replaced."

"No!" Shinji shouted, and Rei looked back to him. "That's not true!" he said, tears flowing openly now. "You can never be replaced!"

Rei was at a loss. She found herself unable to tell him that she had wanted to protect him, even at the cost of her life, and that she could in fact be replaced. For some reason, however, his worry made her feel strange. Perhaps it came from "having a thing" for him. "I…"

"No one can be replaced," Shinji said, cutting her off and dropping his head. Tears fell from his face and onto the bed. He had been so worried, and now she said that she could be replaced? Of all the things Shinji had to tolerate, he couldn't stand Rei thinking that way! Shinji had really liked Rei ever since he had helped from her entry plug after they had defeated the Fifth Angel. That was when he had begun to have feelings for her; feelings that had grown the more time he spent with her and got to know her better. "No matter what you think, no one can be replaced. Your life means more than that!" He looked up at her. "Even if someone brought you back by cloning you, it wouldn't be you! There is only one you!"

Rei was shocked. She didn't know what to say. For the majority of her life, she had grown up hearing the Commander tell her how she could be replaced, telling her how her life didn't matter because of what she was. But now Shinji was telling her exactly the opposite, saying that her life was as important as anyone else's.

"Ayanami," he said. "Don't ever do that again. I can't remember much after I saw the explosion, but I'm sure the reason I went back to Eva was to try and save you. So, no matter what, don't do that again. I don't want you to die."

"Ikari…" Rei said. She really didn't know what to say. This was the first time anything like this ever happened to her. After a few silent moments, she nodded and said, "I understand."

Shinji smiled and removed his right arm from her should to wipe away his tears. "Good," he said. The he noticed the position he was in. Quickly letting go of Rei's shoulders, Shinji leaned back onto his bed. "I'm sorry!" he said, reverting to his usual self. "It's just… I just…" he stuttered.

"It is all right," she said. "I am… happy you said those things."

Shinji stopped stuttering and froze. Did Rei actually say that she was happy about what he had just said? "Really?" he asked.

Rei nodded. "Ikari," she said. "Do you not remember what happened after you got into Unit One?"

Shinji shook his head. "No," he said. "I don't."

"You defeated the angel," she said. "However, when they tried to retrieve you from Unit One, they found that you had been absorbed into it."

"I was…" Shinji said, trailing off, unable to comprehend what Rei had just told him.

Rei nodded.

"For how long?"

"Thirty-one days."

Shinji just stared at her.

Rei stood up. "I must leave now," she said. "I have tests with Dr. Akagi soon." She walked to the door. "Ikari," she said, stopping at the room's threshold. "When you are out of the hospital, I would like to be in your presence more than I am now." Then she left.

Shinji just sat there in shock.

* * *

Dr. Ritsuko Akagi paced back and forth down in Central Dogma. Her lab coat spread out behind her as she continued to walk from one end of the room, to the other. She was irritated.

Rei was late.

For one thing, Rei was never late and that irritated the doctor. For another, she didn't particularly like the doll and that just made it worse. Why did she have to care for the little wench? Why did _he _care more for the blue-haired, red-eyed doll than he did for her? In her irritation, Ritsuko bumped up against the wall, causing the remote control in her pocket to be accidentally pressed.

Ritsuko was slightly startled when the walls began to rise around her, revealing the tank that they concealed. The tank that held LCL—and Rei's clones.

Her surprise quickly turned to anger as she stared at the dozens of pale faced, red-eyed, blue-haired copies of the pilot of Unit Zero. She hated the dolls floating there, with that blank expression. She hated the ghostly giggling that they emitted. These soulless dolls… she hated them! She hated them and she hated Rei! Because they were here, Rei would never go away! She would never have the commander to her self. She didn't know how many times she had seen him come down here in secret, staring at the Reis. They should all be destroyed!

Without realizing what she was doing, Ritsuko pulled the remote control from her pocket. _Yes,_ she thought. _They should all die! Then he'll be mine!_ Ritsuko pressed a button on the remote control.

Red lights flooded the room, and the blank smiles on the faces of Rei's clones changed into looks of pain, their giggles became screams of pain, and they began to dissolve into the LCL

_Yes,_ Ritsuko thought. _Die, die, die, die, DIE! _"DIE!" she screamed at them, shaking her hands, insane delight plastered all over her face.

Suddenly, the giggling returned, and Ritsuko delight drained from her face, as she watched Rei's clones begin to regenerate their lost body mass.

"No!" Ritsuko said aloud. "This isn't possible!" She jammed her finger down on the control again. They needed to die.

This time, the giggling grew louder, and Ritsuko's pounding on the remote control slowed as she watched the changes taking place before her, horror appearing on her face.

Rei's clones no longer had a blank expression. They were smiling, still, but now the smile struck fear into Ritsuko. She didn't know why, they still had the same, soulless eyes, but… all the eyes were fixated on her. Ritsuko slowly backed away from the tank. The laughter from the clones now had a chill to it that it hadn't before.

Suddenly Ritsuko heard a thump behind her, and she whipped around to see that there was a clone staring at her from the other side of the tank she had bumped up against. It was staring straight at her. Ritsuko watched as it lifted an hand and then pounded a fist against the edge of the tank.

Ritsuko slowly backed toward the door. The clones had never acted like this before. They had only floated there, smiling, but now… now they were moving on their own.

Ritsuko watched in horror as all the clones swam up to the wall of the tank, pounding against the wall. They were trying to get out.

Ritsuko felt her pulse rising, and she tried to calm her self. It was fine. Though this was abnormal, the clones couldn't escape the two-foot wall of bullet proof glass.

That was when a crack appeared in the glass.

Ritsuko opened her eyes wide. No, this couldn't be happening. The red light began flashing, and Ritsuko looked to the computer display on the wall. The tank was being eaten away from the inside of the tank for no apparent reason. _This can't be happening! _Ritsuko thought. She was scared, more than she had ever been before. Ritsuko began jamming her finger on the remote control again, trying to destroy these… things before they escaped.

It had no effect, and all the clones had gathered around the crack that had appeared, and they were all banning on the glass, and each and everyone had on a feral grin and their eyes were locked on Ritsuko.

The LCL began to leak from the tank, and Ritsuko ran from the room, shutting the door behind her. Not pausing a moment to rest, she began to run as fast as she could.

She had programmed the MAGI. She knew what would happen as a result of this event. She needed to get out of here, now!

Ritsuko ran. Fast.

* * *

"What the hell is going on? Is it an angel?" Misato yelled as soon the alarms went off. The purple haired major had just gotten a can of beer as she entered the faculty lounge in NERV when a red light began flashing and a klaxon appeared.

"I'm not sure, Major," Maya said as her fingers ran over the keys in front of a computer terminal. "The MAGI aren't telling me anything!"

"Well find out what is happening!" Misato yelled, before turning to the other two workers who had just stood up.

"Aoba, Hyuga," she said, pointing to them.

"Yes, Major?" they asked.

"Get to your stations, quick!"

"Yes!" they yelled and began to run for the door.

"Wait!" Maya said, her eyes widening in fear as she looked at the computer display in front of her.

"What is it, Maya?" Misato asked.

Maya turned to Misato, pale faced. "The MAGI have detected contamination in Central Dogma," she said. "NERV is being locked down in attempt to contain it. If we don't get out of here now, we'll be locked in!"

Misato's face-hardened. "You three," she said, "get out of here now!"

They ran, but Hyuga hesitated at the door.

"What about you, Major?" he asked.

"I'll be right behind you," she told the technician.

Hyuga hesitated for a second, before nodding. "Alright," he said. "Just make sure you get out of here, Major."

Misato smiled. "I will," she said.

Hyuga nodded, and then began to run.

Misato turned to the computer terminal. She needed to warn everybody, now. Pressing a few buttons on the control panel, Misato began to speak.

"This is Major Katsuragi," she said, her voice broadcasting throughout NERV. "There has been a contamination in Central Dogma! All personnel, Evacuate. I repeat, all personnel, evacuate!"

* * *

The commander stood up in his office, after hearing the Major's broadcast. The flashing red light accented his hard features and reflected off the pair glasses he wore. This was most unfortunate.

"We must evacuate, sir." Fuyutsuki said. The older man saw the commander—his former student—tighten his white gloved-hands into fists. This could ruin everything that the commander had been working for.

The commander began walking toward the exit, clamping his hands behind his back. "As soon as we are out," he said, "I want a temporary headquarters set up, and find out the cause of this."

"Yes, sir," Fuyutsuki said as they stepped into an elevator taking them to the surface.

The commander stood silently. The amount of rage contained within was so great that it began to show on his face. If his plans failed as a result of this, whoever caused it would pay dearly.

* * *

Rei had just stepped through NERV's high security doors when she noticed the red alarm light flashing. Something was wrong. She turned to leave, and swiped her card through the reader in attempt to leave. The door didn't open. She tried again, and still got nothing. Something was defiantly wrong. Turning around, she went to find another way out of headquarters.

As she came to the hallway, she watched as the multiple blast doors began sealing it off. Turning, Rei ran in a different direction to try and find another way out.

Suddenly, gas sprayed out from the walls. Rei did her best to hold her breath, but she began to feel woozy. The strength in her legs buckled, and she fell to the floor.

As she slowly faded from consciousness, Rei felt despair. She didn't know why, but something about this scared her. She didn't want to leave Shinji now…

For a moment, she felt something tingle in her abdoman, and then she lost consciousness.

* * *

Shinji was feeling real happy after his conversation with Rei. She had promised to stay alive, and although he hadn't actually come out and said it, he had come pretty close to telling her exactly how he felt about her. Maybe there was hope for him yet. And she has said that she was happy to hear his words!

Suddenly, Shjinj felt a shiver run down his spine. He didn't know what it was, but it gave him a bad feeling. He shook his head. He didn't want to be feeling bad after talking to Rei, especial after she said that she'd like to spend more time with him.

He was sure that she hadn't meant anything by it. After all, there was no reason for her to like him, but it was nice to know that she was opening up more, and getting away from his father.

Shinji fell back onto his pillow. He was tired. It must have been really tough being inside Unit One for so long, though Shinji didn't understand why. He needed some more rest.

Unfortunately, events that would leave Shinji unable to rest for a very long time had already been set in motion.

* * *

**Author's Note:**

_I will most likely re-write this chapter at a later date, partly because I didn't how some bits were worded, and partly because the chapter was too short for my liking. I just wanted to at least start writing this idea so I wouldn't keep putting it off. Anyways, on tothe Angel's Heart Chapter 8!_


	2. Chapter One

**Chapter One**

"Damn that Ikari," one of the members of SEELE said as he slammed his fist down on the table. "He has caused more trouble than he is worth."

"I agree," said another, thin-faced member. "The losses that Ikari has incurred the project have been staggering, and the schedule has needed to be constantly altered because of his meddling."

Chairman Lorenz Keel spoke up, staring at the other members of the Council from behind the visor he wore, enabling him to see them. "Yes, Ikari has shown reluctance to follow orders. Regardless, he gets the job done. Everything that has happened has been laid out in the Dead Sea scrolls. While Ikari hasn't been following our dictations, he has been following the directions of the scrolls."

"However," said a rather large man as rubbed a finger over his moustache, "this event was not laid out in the Scrolls. This could ruin everything that we've worked for."

"That is true," the thin-faced man said again. "If Ikari had followed our orders in the first place, this never would have happened. We have nothing to gain by keeping him."

"We cannot lose him just yet," Chairman Keel said. "He has the loyalties of NERV personnel, which includes the Children. We cannot lose the children. At the moment we are stuck with Ikari."

"Loyalties can be remade," said another member. "They needn't even know that he's gone. We don't need their loyalty, just their work."

"True," Keel said. "We'll see how this all turns out. Ikari is the only one who can fix this problem now."

The council nodded their heads in begrudged agreement. No matter how much they wanted Ikari gone, what the chairman said was true. They needed him to get out of this mess.

"However," said the chairman, "We cannot let him know this. Keep him thinking that he is on the edge. That will make it easier to control him."

"Agreed," came the collective answer from around the table.

"He's coming," the chairman said, and all heads turned to look at the end of table.

A white spotlight flicked on above the end of the table, showing Gendou Ikari now sitting there, his hands folded in front of him as he looked at the council through his glasses.

"This does not bode well for you, Ikari."

Gendou looked over his hands and to the head of the table, where the man who had spoken was sitting. Chairman Keel looked straight back at him.

"Now tell us," the Russian member of the council said, staring straight at Gendou, "how exactly all of this happened."

Gendou glanced at the Russian and met his gaze coolly. "As I have already said, at the moment we have no knowledge as to what happened. All we know is that the Magi detected contamination in Central Dogma and locked down NERV to contain it."

"Could the contamination have been an Angle?" said the member sitting next to the Chairmen.

Gendou moved his gaze to the British man who had just spoken. "It is entirely possible," he said. "However, the Magi did not detect any Angelic signature before locking down. At this point in time, that is still unknown."

"You are treading a thin line here, Ikari," another member said. "First with the awakening of Unit One and now this. All of the Evangelions are out of our reach. If an Angel attacks now, we will be defenseless. What are you going to do about this?"

"I have begun assembling a team to infiltrate NERV and find out exactly what happened. NERV was built to defend against Angels, not against humans. They should have no trouble getting in."

"This is your last chance, Ikari. If you mess up this time, we will remove you from the command of NERV."

Gendou's face remained stoic. He knew what it would mean for them to "remove" him. "Do not worry," he said, standing up. "I will be leading the team myself. If something goes wrong, you won't need to remove me."

Heads around the table nodded their approval.

"Very well, Ikari," Chairman Keel said to him. "This meeting is over."

The lights above every member except Gendou and the chairman went out, leaving the two remaining men staring at each other.

"You had better succeed Ikari," he said. "If you don't, all of this will have been for nothing." As he finished talking, the light above him went out and he vanished.

Gendou stood looked out over the table in silence. "I know," he said, though there was no one listening. He turned around, and walked out of the light.

* * *

"Report, Major," the Commander said.

Misato Katsuragi looked up at the Commander. She knew that he wouldn't be pleased by the news. After NERV had been evacuated, he had ordered her to find out everything she could about what happened.

"We still do not know exactly what happened, Sir," she said. "Only that the Magi had considered the contamination in Central Dogma to be enough of a threat to sacrifice all members of NERV to keep it contained. It was a failsafe that Dr. Akagi had built in incase an angel were to infiltrate Central Dogma." She mentally thanked Maya for telling her about that. "All entrances to NERV have been sealed of; however, after consulting the layout and designs of headquarters, I believe that it would be possible to enter NERV, get to the Magi, and reprogram them to end the lockdown. I highly suggest that we take this action."

Gendou nodded. This had been what he had expected. "How many personnel are unaccounted for?" he asked.

"Three hundred and seven," Misato said, trying hard not to wince at the size of the number. "All but two of whom were minor mechanics or janitorial personnel." Misato mentally scolded herseslf. _Like that makes it any better._

Gendou nodded. "And the others?"

Misato took a deep breath. "Dr. Akagi and the Pilot of Unit Zero are no where to be found. After reviewing Dr. Akagi's schedule on her home computer, it appears that Rei had an appointment with her at the time of the lock-down."

Gendou tensed. Dr. Akagi had invaluable knowledge concerning the Magi and the Evangelions. It would be unfortunate to lose her, but she was not irreplaceable. However, if Central Dogma was indeed compromised, and Rei was lost, the completion of the Project would be impossible."

"Major Katsuragi," Gendou said sternly, "I have assembled a team to infiltrate NERV and do just as you have suggested. I want you to do the same, and assembled a team of the most capable people you have."

"Sir?' Misato said. "Who is going to lead the other team?"

"I am," the commander said.

Misato was taken aback. She hadn't expected this. "But Sir—" she began, but he cut her off with a sharp gesture.

"This is non-negotiable," he said.

Misato repressed her objection and nodded. "Yes, Sir!"

"Your objective will be to get to the Magi and reprogram them," he said.

"But what about Dr. Akagi and Rei?" Misato asked.

"My team will facilitate the location and retrieval of Dr. Akagi and the Pilot of Unit Zero. Understand?"

"Yes, Sir," Misato said, breathing easier. At least he wasn't abandoning them.

"Very well," the commander said. "Assemble your team. Dismissed."

Misato nodded her head, saluted the commander, and walked out of the room.

As the door to the temporary command center, created above ground in case something like this ever happened, closed behind her, Misato leaned against the wall and sighed. She closed her eyes. This was horrible. How could something like this have happened? She hopped that Ritsuko and Rei were alright, wherever they were.

"This sure is a nasty business," someone said.

"What do you want, Kaji," Misato said, without opening her eyes.

"Just to talk," he said. "You're not like the commander, Misato. You care about all the people that were lost down there."

"Shut up Kaji," Misato said, opening her eyes, and turning to look at him. "You better not have had anything to do with this."

"This time I'm as lost as you are as to what happened," Kaji said, frowning. "I don't like not knowing what's happening." He shook his head. "This has been one hectic day."

"Tell me about it," Misato said. "It's only an hour before midnight and I have to assemble a team to infiltrate NERV and reprogram the MAGI. Want to help?"

Kaji looked at her in surprise. "I would love to, but the Commander has already recruited me for another team for the same thing. He's the one leading it as well."

Misato shook her head. She should have known that the commander had taken Kaji. Everyone seemed to know that he was a spy, and because of that, he knew all the back ways into NERV. "Not any more," Misato said. "The commander gave that mission to me. His team has a new objective."

"What is it?" Kaji asked.

"Your team is now looking for Rei and Ritsuko," Misato said, brushing some hair out of her face. "Rei is one of the Children, and no one knows the MAGI better than Ritsuko. Retrieving them has become top priority apparently."

Kaji nodded. "I see. Well, since I can't go with you, how about I give directions on the best way to get to the MAGI?"

Misato smiled. "Not that you actually know anything, right?"

Kaji smiled. "Of course. I could have gotten the directions anywhere."

Misato nodded. "Alright," she said. "Give them to me as soon as possible. I need to go assemble my team." She started to turn to go, but Kaji stopped her.

"Have you told the other Children yet?"

Misato froze in mid-step. She hadn't seen Shinji and Asuka since the lockdown. Section 2 had let her know that they were safe, and that was enough. Now that she knew that Rei was missing, possibly dead, she couldn't face Shinji and tell him that. She knew that Asuka wouldn't take it as hard, but she didn't know about Shinji.

"No," she said. "I don't think I can tell Shinji."

Kaji came up behind her. "Misato. You can't keep it from him forever. Remember what happened last time you couldn't tell him something?"

Misato winced. Last time she hadn't told him that his friend Touji Suzuhara was the Fourth Child. If she had only told him, things might not have happened like they had when the Thirteenth Angel attacked.

"Go tell him," Kaji said. "He deserves to know."

Misato turned around and looked up at Kaji.

"I saw him right before he went to fight last time," Kaji said. "We were in a park down in the Geofront, and we could see the battle against the Fourteenth Angel. Shinji didn't think that he could get back into the Eva, even though he wanted to save everybody. That was when Unit Zero came out, carrying that N2 mine. I watched as Shinji stared at what happened. When the mine exploded, he screamed. I can't describe to you the look of anguish, suffering, and fear that covered his face. Then he took off, running as fast as he could towards the command center. I got a last look at his features before he left though. It was pure hate."

"That's why he got into Eva?" Misato asked.

Kaji nodded. "Yes," he said. "He thought that Rei had been killed, and went to kill the angel. I'm sure of it. There was no desire to save people then. He hated the angel. Every fiber of his being was focused on killing it. It is that, I believe, which caused the Eva to awaken." Kaji looked away for a second and shivered. "He scared me." Then he looked down at Misato. "You understand why you must tell Shinji what happened," he said. It wasn't a question.

Misato nodded. "Alright," she said. "I'll go tell him right now."

Kaji put a hand on her should and squeezed. "Good luck."

Misato smiled and then turned around, walking towards the hospital.

"He is sleeping right now."

"I'm sorry, but I really need to speak to him."

Shinji woke to the sound of Misato's voice. Yawning and rubbing the sleep out of his eyes, he sat up. "Misato?" he said, looking to the door on his right.

He saw Misato talking to the doctor. She looked at him when said her name, said something to the doctor, and then walked over to him. The doctor closed the door behind them.

"Shinji…" she said as she reached the bedside.

"Yes, Misato?"

"How are you doing?" Misato said, forcing a smile as she took a seat in the chair next to his bed.

"I'm fine," he said, yawning again. "Ayanami told me that I had been absorbed by Unit One for a month. I can't remember it though. Everything after the N2 mine exploded seems all fuzzy."

"That's alright," Misato said. _Kaji must have been right._ "The doctor says that you'll be fine."

"That's good," Shinji said, smiling.

Misato saw his smile and faltered. _Oh my God… what is this going to do to him? I can't tell him. I just can't!_

Shinji saw something and frowned. "Is everything alright, Misato?" he asked.

"I…" Misato started, but she stopped. There was a strange pain the back of her thought, and she couldn't get the words out. She blinked her eyes as she felt tears beginning to form.

"Misato!" Shinji said, reaching out to her. "What's wrong?"

"It's…" she began again, before squeezing her eyes shut as she felt the tears begin to fall. "I'm sorry, Shinji!" she said, gasping to get the words out. She put her face down on the bed to burry her sobs. "I'm sorry, Shinji! I'm so sorry!"

"Misato!" Shinji said, grabbing a hold of her. "What's wrong Misato?"

Misato slowly lifted her head, and looked at Shinji. "It's Rei," she said in a whisper.

She saw Shinji's eyes widen in alarm. "What happened?" Shinji asked. "Is she alright?"  
Misato shook her head. "We don't know," she said through sobs. "Something happened in Central Dogma and the MAGI quarantined headquarters. We haven't been able to locate Rei since."

She felt Shinji slowly let go of her, and she looked up at him.

He had his eyes squeezed shut and his hands clenched. He was mouthing something voicelessly. Misato whipped away her tears and tried to make out what Shinji was saying.

"No, this can't be happening. This can't be happening. This can't be happening!" That's what he was saying. _Shinji,_ Misato thought. _I'm so sorry._

Suddenly Shinji opened his eyes. "Are there people going to look for her?" he asked in a whisper.

Misato nodded. "The commander is leading a team of people to go and search for her and Dr. Akagi."

"My father?" Shinji asked.

Misato nodded.

Shinji got out of the bed.

"Shinji!" Misato said, standing up in alarm. "What are you doing?"

"I'm going to help find Ayanami," he said as he slipped on the slippers the hospital left him.

"But Shinji, you need to stay here and recover!"

"Don't try and stop me Misato," he said in an emotionless voice as he walked towards the door. He turned and looked at Misato. "I will find Ayanami."

Misato was taken a back at Shinji's expression. He looked so much like the commander, and it scared her. She didn't know why, but she knew that she would not be able to stop him.

She nodded. "Alright Shinji," she said as she walked up next to him. "I won't."

When the door opened and Shinji and Misato walked out, the doctor looked surprised. "Hey!" he said, walking up to Misato. "You can't take him anywhere right now!"

Misato looked at him. "He is needed at NERV headquarters," she said. "No exceptions."

"He is a sick boy and needs to recover," the doctor said. "I cannot let you take him."

Misato was about to say something back to the doctor, when Shinji spoke up. "I am fine," he said. "Now let me through."

"I'll be the one to decide that," the doctor said, impatiently tapping his foot. "Now, you will return to that room until I clear you for removal."

Misato sighed and pulled out her gun. _I can't believe I'm doing this._ "He is leaving. Now."

The doctor dropped the clipboard and jumped back, hands in the air. "Of course," he said, forcing a smile. "I was just about to say how healthy he looked."

Misato nodded her head. "Of course you were." Then she put the gun away and said, "Let's go, Shinji." Then they walked down the hall and out of the hospital, leaving a breathless doctor behind.

Once they were in the temporary headquarters for NERV, Shinji said, "Thank you, Misato."

"Don't mention it," Misato said. "Think of it as payment for saving the earth so many times."

Shinji nodded.

Misato looked at him, and noticed that he was still wearing a hospital gown. "Um, Shinji," she said. "Do you want to change clothes first?"

Shinji shook his head. "I'm going to see my father now."

Misato just shrugged and kept walking.

"We're here," she said as they reached the Commander's temporary office.

Shinji nodded, and began to walk in.

"Hey!" Misato sputtered out. "Wait! He might be having a meeting!"

Shinji didn't listen and pushed open the door, walking into his father's office.

As soon as the door opened, Shinji looked into the office. The commander and his team stood in the middle of the room, looking over a spinning holographic representation of NERV that floated above table. Kaji was pointing out the best way to search NERV in the shortest time possible. "If we can get to one of the main terminals," Kaji was saying, "we can scan headquarters for—" he cut off when he noticed Shinji, and looked up.

The Commander, having noticed this, followed Kaji's gaze and saw Shinji standing there in a hospital apron.

"Father," Shinji said, staring at him straight in the face.

"What are _you_ doing here?" he asked.

"I want to help find Ayanami."

"Impossible," Gendou said. "You would only hinder the operation. You are an Evangelion Pilot. You are not suited for this."

"I want to go," Shinji said again, not looking away from his father.

Gendou fell silent. Something about the way Shinji looked at him was familiar. He couldn't place what it was, but it felt familiar. Like something he hadn't seen a very long time.

The Commander had no mirrors in his office, no mirrors in his quarters, and he did not look in mirrors in the bathroom. He couldn't stand to look in a mirror and see his face, reminding him of everything that he had lost. If the Commander had looked in a mirror, he would realize that what he saw in Shinji's face was exactly what people saw in his own.

Something about the way Shinji was, the way he looked at his father, the way he stood, said something to Gendou. He knew that Shinji would go looking for Rei even if he didn't have permission. Gendou stared at his son.

"I'm sorry, Commander," Misato said as she ran in. "He insisted that he come here."

"Please, Father," he said in a whisper. "I want to save her."

Gendou stared at Shinji a moment longer. If Shinji did indeed go after Rei by himself, he would certainly die. Shinji was one of the rare few that could pilot the Evangelions. Unit One had already shown that it would accept no other pilot. Unit One would be lost if Shinji were to die. The Commander could not have that. Even if he had Shinji restrained, there was always the chance that he might escape, and if the mission ran foul… well, it wouldn't matter then anyway. And then there was… something else that Gendou couldn't explain, something that told him to bring Shinji with them.

Gendou nodded. "Alright," he said, causing several jaws in the room to drop. "But understand this. On this mission you follow my orders _exactly_. If you get in the way, or refuse to follow an order, you _will_ be escorted to the surface. Do you understand, Shinji?"

Shinji nodded. "I do, father."

Gendou grunted in approval. "Come here," he said. "We are going over the plan of attack."

Shinji nodded and walked over to the table, where the rest of the team was trying to recover from the events that just happened.

"Major Katsuragi. " he said, looking at Misato. "Have you assembled your team?"

Misato closed her mouth and shook her head. "No, Sir."

"Then I advise that you do so right away."

Misato nodded. "Yes, Sir," she said. Then she turned and left the room again.

The Commander looked down at Shinji, who was at the other side of the table looking down on the layout of NERV. This was going to be interesting.

The Commander glanced at Kaji, who nodded.

"As I was saying," he said, "if we can get to one of the main terminals to the MAGI, we can run a scan of headquarters, searching for Dr. Akagi and the First Child." He pointed to several spots on the hologram, which then lit up and showed them details. "The only problem is that we can't easily get to one of the main terminals. All the entrances that aren't impenetrable are as far away as they can possibly be, and with the lockdown, it will be even harder to cover that distance, and let's not forget that we don't know what is down there."

Shinji was looking at the diagram. He understood what Kaji was saying. He had seen the many blast doors would close if there were ever an emergency like this. He knew that it would be really hard to get into NERV. But…

"What about this?" he said, causing everyone to look at him. No one had expected Shinji to speak up. It just wasn't his way. Then again, standing up to his father like this wasn't his way either.

Shinji realized that everyone was looking at him and attempted to shrink back before he caught himself. _No,_ he thought. _I need to help save Rei. I will do everything I can to save her._ He reached out to the hologram like he had seen Kaji do and touched a certain spot. It lit up and zoomed in on the place Shinji had touched, displaying data.

Kaji looked over what Shinji had shown them with approval and mild surprise. "Yes," he said, unable to believe that he hadn't thought of this. "Yes. This will do nicely." He looked down at Shinji. "How did you know about this."

Shinji looked up at him, avoiding the gazes of the people around him. The adrenaline he had felt was beginning to slowly wear off now, and he was conscious of the people around him.

"I see them every time the Eva is launched," he said. "They fly by as I'm being taken up to the surface."

Kaji nodded. "I see," then he turned to the rest of the team, and gestured to the hologram. "These vents connected to the Eva launch shaft are all interconnected and lead deep into headquarters. While they do not bring us directly to one of the main terminals, they bring us very close." He looked back to Shinji. "Good job."

Shinji smiled.

Then Gendou spoke. "Yes," he said. "Good work Shinji." Then everyone stared at him as he leaned over the table, looking at the hologram.

"Thank you," Shinji said quietly.

Gendou just grunted in response. Something was wrong about those vents. They had been placed too conveniently. There were no sensors in the vents either. It was almost as if someone had _wanted _a way into NERV without being detected. He was going to have to look into this later.

"Alright," the commander said, straightening up. "We'll cut a whole through the doors leading to this Launch Shaft from above," he said, pointing to one of the launch shafts. "Using ropes, we'll climb down to the vents, enter them, and then make our way to the terminals." He looked around at his team. "Does everybody understand?"

"Yes, Sir!" they all said in unison, though Shinji was a little behind.

"Good," Gendou said. "We will begin at 0600 hours. Until then, prepare yourselves. Dismissed." He deactivated the hologram.

As the team began leaving, Gendou turned to Shinji and Kaji. "You two stay here."

Kaji and Shinji nodded as they stopped and watched the rest of the team stream out. Once everyone had left, Gendou looked at them.

"Shinji," he said. "You understand what you must do. Every order I give, you must follow. If you jeopardize the mission in any way, you will be abandoned." Of course, he couldn't abandon Shinji. Unit One wouldn't activate without him. But there was no need to let Shinji know that. As long as he thought he would be left behind, that was enough. He looked straight at Shinji. "_Every_ order. Understand?"

"Yes, Father." Shinji said without hesitation. He was going to save Rei. He was.

Gendou nodded, and then turned to Kaji. "Inspector Kaji," he said. "You will be in charge of Pilot Ikari for the duration of the mission. You will stay with him at all times."

"Understood, Commander," Kaji said.

Gendou looked at a display showing the time. "There are six hours before we move out," he said, looking at Kaji. "In that time, I want you to train Pilot Ikari in self defense."

"Yes, Commander."

"Good." Gendou turned and looked at Shinji again. "Every order." He turned around and gestured to them. "You are dismissed."

Shinji and Kaji nodded, and then they both turned and left the room.

"That was a good job, Shinji," Kaji said as he drove down the road. Then he laughed. "I can't believe that I never noticed that before. It's such a perfect way into almost everywhere in NERV."

"You're welcome, Kaji," Shinji said. "I always wondered what those were every time the Eva was launched. I never thought that they'd be that useful."

"Shinji," Kaji said, smiling as he drove, "your speech might have just influenced the outcome of this mission." Kaji looked out a the windshield for a moment, and then said, "You know Shinji, you weren't acting like your usual self today."

"Yeah," Shinji said, looking away, "I know."

"Any idea on what caused this sudden change?"

"I don't know," Shinji said. "When I heard that Ayanami was missing, I just… I don't know. I wanted to save her no matter what."

Kaji nodded. "I thought it might be that. Do you remember what happened back when the Fourteenth angel was attacking, Shinji?"

Shinji looked back to Kaji. "I don't remember much. I just remember seeing the mine explode, and then everything gets fuzzy. I mean, it's like seeing everything from the corner of your eye, where you can tell that something is happening, but you don't really know what unless you turn to look at it."

"But you couldn't turn to look at it?" Kaji asked, still driving.

Shinji shook his head. "I don't think I wanted to. Something… I don't know. Something told me that I didn't want to see what was there."

"And did that happen again today? With your father?"

"No. Today was different. I don't know, it was like I didn't care what happened. It wasn't the same."

Kaji nodded. "Well, at least you've already done the hardest thing."

"I have?" Shinji asked, confused.

"Yup. I don't think anything can be much harder than going up against the Commander like that." He grinned at Shinji, and Shinji smiled back.

"So, um, where are we going?" Shinji asked, looking out the window.

Kaji jerked his head towards a building that they were approaching. "It's Section 2's headquarters. They have one inside and outside of NERV, in case something like this ever happens." Kaji let out a small laugh. "I bet they never thought that they'd really need it."

"Um, Kaji," Shinji said, looking at the building that they were approaching. "Why are we going there?"

"They have a shooting range there." When Shinji still had You heard your father, didn't you?" Kaji looked over at Shinji. "I've got to train you in self defense." He looked back to the road. "And when _your_ father says that, it means that you're gonna need to learn how to use a gun."

"A gun!" Shinji said in alarm. "I'm going to have to use a gun!"

"It's for protection, Shinji. You're going to have to learn how to use one anyway."

"B-but I don't want to hurt anybody!"

Kaji sighed. "Shinji, sometimes you have to hurt others in order to keep yourself safe. You don't have to kill them, but if you want to survive you will need to disable them. However, sometimes you won't have that choice. If you want to live, sometimes you have to kill." Kaji glanced at Shinji and saw him staring at his lap. "Or," he began, "you might have to shoot in order to protect someone else."

Shinji looked up.

"You want to protect Miss Ayanami, don't you Shinji?"

"Yes…"

"You wand to keep her out of a hospital gown like the one you're wearing?"

"Yes…"

"If you want to protect her outside of an Eva, you're may need to use a gun."

"But why?"

Kaji sighed. He couldn't tell Shinji everything. He wasn't even sure if everything he knew was true. Most of it was all speculation. There was no guarantee that he was right, since all of it was just pieces he had been able to puzzle together from looking at confidential files. "Shinji," he said slowly, "I think… that sometime in the future… maybe in a few months, maybe in a few years… Miss Ayanami might be in danger."

"What are you talking about?" Shinji said looking straight at Kaji.

"I'm not sure Shinji. I might be wrong, but I don't know. Do you really want to take the chance?" He pulled into the parking lot by Section 2's headquarters, found a spot, and turned off the car. He looked over at Shinji. "We're here."

Shinji looked at Kaji for a moment. "Alright," he said, opening the door. "Let's go."

Kaji nodded and opened his door. "Right then," he said, flashing a grin. "You're the boss."

* * *

"What do you mean Shinji's going to infiltrate NERV!"

Misato closed her eyes as she put a hand to her forehead and massaged her temple. _I really don't need to deal with this right now._ "Asuka," she said to the angry redhead in front of her. "Shinji is going there looking for Rei. She was trapped inside when NERV locked down and Shinji is worried about her."

"Why is he worried about that doll?" she said.

"Rei is his friend Asuka. He would do the same for you if you were stuck down there."

"But I'm not stuck down there. She is, and he's going after her!"

Misato massaged her temple harder. _Damn it Asuka, stop being so close-minded. The world does not revolve around you._

Suddenly Misato felt something right in front of her and opened her eyes. Asuka was staring straight at her.

"Take me with you, Misato," she said.

"Asuka!" Misato said, jumping back a little.

"Take me with you!"

"Asuka, I can't," Misato said, recovering a little bit. "I can't put you in that kind of danger. We don't know what might be down there!"

"You let Shinji go!"

"He got the Commander's permission."

"That's because he's the Commander's son."

"You know that's not true, Asuka."

"Please Misato," Asuka begged. "I won't be any trouble, and I already know how to use a gun. They taught me how to use one back in Germany."

"I know Asuka, but—"

"Shinji gets to go, why can't I?"

"Asuka—"

"Let me go Misato, please!"

Misato sighed. She really didn't need this. "Alright, Asuka," she said. "But if you go, you must do everything I say. No acting on your own, and you stay with me. If you stray from us or go do something without my approval, I will send you back to the surface. Understood?"

"Yes!" Asuka yelled as she jumped up, thrusting her fist into the air. "Thank you, Misato. I promise to follow your orders! I'll show Shinji he isn't the only one who can be a hero!"

Misato closed her eyes and began massaging her temple again. _Oh boy. This was going to be one hell of a day._

* * *

When Rei opened her eyes, everything was flooded in red light. Moving slowly, she pushed herself into a sitting position, and let out a small groan. Her head hurt. She put a hand to her forehead, pushing her hair out of the way.

_What is this?_ She thought. _Where am I?_

Moving her hand, she raised her head and looked around.

She didn't recognize any of it. Where was she? For that matter, who was she? She felt a creeping fear as she realized that she had no idea where she was. She stood up and looked around. She didn't know why, but she felt that she needed to get out of here. Something was calling her. She took a step toward the wall, bent down, and opened up a vent before crawling into it.

She didn't know what or who was calling for her, but it felt familiar, and familiarity was something she needed at the moment, with no memory of who she was.

* * *

The acid fell down into the launch shaft as it finished melting a two-meter wide whole in the cover. The two men in yellow suits stepped back from the whole, taking the container of acid them.

Shinji stood with his father and Kaji, overlooking the operation. He watched as the men began setting up a system of pulleys, harnesses, and ropes that would let them descend safely into the shaft.

Shinji turned and looked at the sun, rising steadily into the sky. It was only a few hours after dawn. Though his hands weren't touching it, he could feel the wait of the gun at his side. His right hand clenched and unclenched and he thought about having to use it. Kaji had said that he was a natural. Shinji didn't know if he was comfortable knowing that.

They were almost done setting up the pulley system. Soon they would be descending into the depths of NERV to find out what happened. Shinji's hand clenched again. Rei was down there somewhere, and he didn't know if she was hurt or alright. He would save Rei.

He would.


End file.
